Pause Sites Promote Transcriptional Termination of Mammalian RNA Polymerase II

Abstract

Polymerase II (Pol II) transcriptional termination depends on two independent genetic elements: poly(A) signals and downstream terminator sequences. The latter may either promote cotranscriptional RNA cleavage or pause elongating Pol II. We demonstrate that the previously characterized MAZ₄ pause element promotes Pol II termination downstream of a poly(A) signal, dependent on both the proximity of the pause site and poly(A) signal and the strength of the poly(A) signal. The 5′→3′ exonuclease Xrn2 facilitates this pause-dependent termination by degrading the 3′ product of poly(A) site cleavage. The human β-actin gene also possesses poly(A) site proximal pause sequences, which like MAZ₄ are G rich and promote transcriptional termination. Xrn2 depletion causes an increase in both steady-state RNA and Pol II levels downstream of the β-actin poly(A) site. Taken together, we provide new insights into the mechanism of pause site-mediated termination and establish a general role for the 5′→3′ exonuclease Xrn2 in Pol II termination.